Intertidal seagrass meadows are important coastal habitats that retain organic carbon within their biomass and underlying sediments. Yet these ecosystem services, especially total organic carbon (TOC) content in surface sediments, can vary across space and time through interactions among episodic seagrass growth, tidal gradient, sediment properties, and extreme weather. We investigated the associations between environmental variables, seagrass presence, loss, and natural recovery with both longer-term and event-scale surface sediment carbon dynamics at San Tau and Pak Nai, Hong Kong. Five fixed points at two shore positions were sampled during eight periods from January 2023 to September 2025, with additional sampling following two typhoons (Whipa, Ragasa) and an extreme-rainfall episode in 2025. Seagrass cover and sediment texture were quantified, and surface sediments (0–5 cm) were analysed for TOC, nitrogen contents, δ15N, and δ13C isotopes. At San Tau, seagrass cover changed episodically, allowing comparison among meadow development, complete cover loss, and partial high-shore recovery. Multivariate analysis associated TOC most closely with seagrass cover, and cover loss coincided with a 46% decline in mean high-shore TOC. Slow recovery of carbon stocks was observed with seagrass recovery. Pak Nai remained mostly unvegetated, and TOC was closely associated with silt and clay, and the finer low shore generally retained more TOC than the sandier high shore. At Pak Nai, high-shore sediments became gradually sandier, suggesting weaker sediment stabilisation and reduced retention of fine particles and associated organic carbon. However, after extreme events, responses were limited: no significant reduction in seagrass cover was detected at San Tau, while its vegetated high shore maintained higher TOC than the unvegetated low shore after each event. Pak Nai showed no clear event-related change. Together, these observations distinguish a vegetation-linked carbon-retention pathway at San Tau from a sediment-texture-linked pathway at Pak Nai. Surface sediment carbon dynamics therefore depend on local shore and sedimentary context, while seagrass remains important through vegetation-associated organic matter retention and its broader role in sediment stabilisation and habitat structure.